From a240f5e8a450855fdf7411ac4c7889d7352388ea Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 9 Aug 2017 14:21:21 +0200
Subject: [PATCH 01/11] Minor backwards-compatibility thing

---
 bismark.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bismark.nf b/bismark.nf
index f988c72e..ceecd54f 100644
--- a/bismark.nf
+++ b/bismark.nf
@@ -569,7 +569,7 @@ workflow.onComplete {
     if(workflow.commitId) email_fields['summary']['Pipeline repository Git Commit'] = workflow.commitId
     if(workflow.revision) email_fields['summary']['Pipeline Git branch/tag'] = workflow.revision
     if(workflow.container) email_fields['summary']['Docker image'] = workflow.container
-    email_fields['summary']['Nextflow Version'] = nextflow.version
+    email_fields['summary']['Nextflow Version'] = workflow.nextflow.version
     email_fields['summary']['Nextflow Build'] = workflow.nextflow.build
     email_fields['summary']['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
 

From b36dd14ce52cb182f04a5413fb4784efdc47818e Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Tue, 15 Aug 2017 11:00:06 +0200
Subject: [PATCH 02/11] Remove RNA stuff from MultiQC config.

---
 conf/multiqc_config.yaml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/conf/multiqc_config.yaml b/conf/multiqc_config.yaml
index bf9c4d07..0794c3bf 100644
--- a/conf/multiqc_config.yaml
+++ b/conf/multiqc_config.yaml
@@ -6,6 +6,3 @@ report_comment: >
     analysis pipeline. For information about how to interpret these results, please see the
     <a href="https://github.com/SciLifeLab/NGI-MethylSeq/blob/master/docs/README.md" target="_blank">documentation</a>.
 swedac_accredited: false
-report_section_order:
-    ngi-rnaseq:
-        order: -1000

From 1d9344cf4161a2940d6fd8a5abaca854e351d636 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Mon, 28 Aug 2017 10:00:28 +0200
Subject: [PATCH 03/11] Bugfix: Collect bismark index to allow multiple samples
 to aligngs

---
 CHANGELOG.md | 1 +
 bismark.nf   | 3 +--
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 732a4716..ae76aadc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 ## v0.3dev
 * Fix `--rrbs` mode ([#24](https://github.com/SciLifeLab/NGI-MethylSeq/issues/24))
+* Fixed fairly major bug where only a single sample would run past alignment
 * Merged test scripts and rewrote to use command line flags / new travis script.
 * Refactored software version collection code to be more resilient and cleaner / easier to maintain.
 
diff --git a/bismark.nf b/bismark.nf
index ceecd54f..caf11163 100644
--- a/bismark.nf
+++ b/bismark.nf
@@ -67,7 +67,6 @@ if( params.bismark_index ){
     bismark_index = Channel
         .fromPath(params.bismark_index)
         .ifEmpty { exit 1, "Bismark index not found: ${params.bismark_index}" }
-    makeBismarkIndex_stderr = Channel.empty()
 }
 else if ( params.fasta ){
     fasta = file(params.fasta)
@@ -279,8 +278,8 @@ process bismark_align {
         }
 
     input:
-    file index from bismark_index
     set val(name), file(reads) from trimmed_reads
+    file index from bismark_index.collect()
 
     output:
     file "*.bam" into bam, bam_2

From f491c8ac80e57dc47d0d5dd1d583bfd5a59867fa Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 30 Aug 2017 11:48:09 +0200
Subject: [PATCH 04/11] Don't consume software_versions_yaml channel for
 MultiQC. Update docker image for MultiQC version.

---
 Dockerfile | 2 +-
 bismark.nf | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index bc9f191a..7e9da7cb 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -105,4 +105,4 @@ RUN mkdir /opt/MethylDackel && \
     rm /opt/MethylDackel/MethylDackel.zip
 
 # Install MultiQC
-RUN pip install git+https://github.com/ewels/MultiQC.git
+RUN pip install multiqc
diff --git a/bismark.nf b/bismark.nf
index caf11163..d7c6d891 100644
--- a/bismark.nf
+++ b/bismark.nf
@@ -522,7 +522,7 @@ process multiqc {
     file ('bismark/*') from bismark_reports_results.collect()
     file ('bismark/*') from bismark_summary_results.collect()
     file ('qualimap/*') from qualimap_results.collect()
-    file ('software_versions/*') from software_versions_yaml
+    file ('software_versions/*') from software_versions_yaml.collect()
 
     output:
     file "*_report.html" into multiqc_report

From f5dee4e16792b81176e408174f7e734c4132f226 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 30 Aug 2017 16:47:57 +0200
Subject: [PATCH 05/11] Move docker image back to openjdk:8u121 so bowtie build
 works

Also split bwa tools out into own dockerfile to keep things simple
---
 Dockerfile     | 33 ++----------------
 Dockerfile-bwa | 91 ++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 94 insertions(+), 30 deletions(-)
 create mode 100644 Dockerfile-bwa

diff --git a/Dockerfile b/Dockerfile
index 7e9da7cb..a9d21a5c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,5 @@
-FROM openjdk:8
+# openjdk:8 moved from debian jessie to stretch after u131, which breaks everything (bowtie)
+FROM openjdk:8u121
 
 LABEL authors="phil.ewels@scilifelab.se,denis.moreno@scilifelab.se" \
     description="Docker image containing all requirements for NGI-MethylSeq pipeline"
@@ -52,12 +53,6 @@ RUN curl -fsSL https://github.com/samtools/samtools/releases/download/1.5/samtoo
     make install && \
     rm /opt/samtools-1.5.tar.bz2
 
-# Install PicardTools
-RUN curl -fsSL https://github.com/broadinstitute/picard/releases/download/2.0.1/picard-tools-2.0.1.zip -o /opt/picard-tools-2.0.1.zip && \
-    unzip /opt/picard-tools-2.0.1.zip -d /opt/ && \
-    rm /opt/picard-tools-2.0.1.zip
-ENV PICARD_HOME /opt/picard-tools-2.0.1
-
 # Install Bowtie2
 RUN mkdir /opt/bowtie2 && \
     curl -fsSL https://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.2/bowtie2-2.3.2-source.zip -o /opt/bowtie2/bowtie2.zip && \
@@ -82,27 +77,5 @@ RUN mkdir /opt/Qualimap && \
     ln -s /opt/Qualimap/qualimap_v2.2.1/qualimap /usr/local/bin/qualimap && \
     rm /opt/Qualimap/qualimap.zip
 
-# Install BWA
-RUN mkdir /opt/bwa && \
-    curl -fsSL https://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.15.tar.bz2 -o /opt/bwa/bwa.tar.bz2 && \
-    tar xvjf /opt/bwa/bwa.tar.bz2 -C /opt/bwa/ && \
-    cd /opt/bwa/bwa-0.7.15/ && \
-    make && \
-    ln -s /opt/bwa/bwa-0.7.15/bwa /usr/local/bin/bwa && \
-    rm /opt/bwa/bwa.tar.bz2
-
-# Install bwa-meth
-RUN pip install toolshed && \
-    pip install git+git://github.com/brentp/bwa-meth.git
-
-# Install MethylDackel
-RUN mkdir /opt/MethylDackel && \
-    curl -fsSL https://github.com/dpryan79/MethylDackel/archive/0.2.1.zip -o /opt/MethylDackel/MethylDackel.zip && \
-    unzip /opt/MethylDackel/MethylDackel.zip -d /opt/MethylDackel && \
-    cd /opt/MethylDackel/MethylDackel-0.2.1 && \
-    make && \
-    make install prefix=/usr/local/bin && \
-    rm /opt/MethylDackel/MethylDackel.zip
-
 # Install MultiQC
-RUN pip install multiqc
+RUN pip install git+https://github.com/ewels/MultiQC.git
diff --git a/Dockerfile-bwa b/Dockerfile-bwa
new file mode 100644
index 00000000..fa3aac87
--- /dev/null
+++ b/Dockerfile-bwa
@@ -0,0 +1,91 @@
+FROM openjdk:8
+
+LABEL authors="phil.ewels@scilifelab.se,denis.moreno@scilifelab.se" \
+    description="Docker image containing all requirements for NGI-MethylSeq pipeline"
+
+# Install container-wide requrements gcc, pip, zlib, libssl, make, libncurses, fortran77, g++, R
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+        g++ \
+        gcc \
+        gfortran \
+        libbz2-dev \
+        libcurl4-openssl-dev \
+        libgsl0-dev \
+        liblzma-dev \
+        libncurses5-dev \
+        libpcre3-dev \
+        libreadline-dev \
+        libssl-dev \
+        libtbb-dev \
+        make \
+        python-dev \
+        zlib1g-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install pip
+RUN curl -fsSL https://bootstrap.pypa.io/get-pip.py -o /opt/get-pip.py && \
+    python /opt/get-pip.py && \
+    rm /opt/get-pip.py
+
+RUN curl -fsSL http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip -o /opt/fastqc_v0.11.5.zip && \
+    unzip /opt/fastqc_v0.11.5.zip -d /opt/ && \
+    chmod 755 /opt/FastQC/fastqc && \
+    ln -s /opt/FastQC/fastqc /usr/local/bin/fastqc && \
+    rm /opt/fastqc_v0.11.5.zip
+
+# Install cutadapt
+RUN pip install cutadapt
+
+# Install TrimGalore
+RUN mkdir /opt/TrimGalore && \
+    curl -fsSL https://github.com/FelixKrueger/TrimGalore/archive/0.4.4.zip -o /opt/TrimGalore/0.4.4.zip && \
+    unzip /opt/TrimGalore/0.4.4.zip -d /opt/TrimGalore && \
+    ln -s /opt/TrimGalore/TrimGalore-0.4.4/trim_galore /usr/local/bin/trim_galore && \
+    rm /opt/TrimGalore/0.4.4.zip
+
+# Install SAMTools
+RUN curl -fsSL https://github.com/samtools/samtools/releases/download/1.5/samtools-1.5.tar.bz2 -o /opt/samtools-1.5.tar.bz2 && \
+    tar xvjf /opt/samtools-1.5.tar.bz2 -C /opt/ && \
+    cd /opt/samtools-1.5 && \
+    make && \
+    make install && \
+    rm /opt/samtools-1.5.tar.bz2
+
+# Install PicardTools
+RUN curl -fsSL https://github.com/broadinstitute/picard/releases/download/2.0.1/picard-tools-2.0.1.zip -o /opt/picard-tools-2.0.1.zip && \
+    unzip /opt/picard-tools-2.0.1.zip -d /opt/ && \
+    rm /opt/picard-tools-2.0.1.zip
+ENV PICARD_HOME /opt/picard-tools-2.0.1
+
+# Install Qualimap
+RUN mkdir /opt/Qualimap && \
+    curl -fsSL https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.2.1.zip -o /opt/Qualimap/qualimap.zip && \
+    unzip /opt/Qualimap/qualimap.zip -d /opt/Qualimap && \
+    ln -s /opt/Qualimap/qualimap_v2.2.1/qualimap /usr/local/bin/qualimap && \
+    rm /opt/Qualimap/qualimap.zip
+
+# Install BWA
+RUN mkdir /opt/bwa && \
+    curl -fsSL https://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.15.tar.bz2 -o /opt/bwa/bwa.tar.bz2 && \
+    tar xvjf /opt/bwa/bwa.tar.bz2 -C /opt/bwa/ && \
+    cd /opt/bwa/bwa-0.7.15/ && \
+    make && \
+    ln -s /opt/bwa/bwa-0.7.15/bwa /usr/local/bin/bwa && \
+    rm /opt/bwa/bwa.tar.bz2
+
+# Install bwa-meth
+RUN pip install toolshed && \
+    pip install git+git://github.com/brentp/bwa-meth.git
+
+# Install MethylDackel
+RUN mkdir /opt/MethylDackel && \
+    curl -fsSL https://github.com/dpryan79/MethylDackel/archive/0.2.1.zip -o /opt/MethylDackel/MethylDackel.zip && \
+    unzip /opt/MethylDackel/MethylDackel.zip -d /opt/MethylDackel && \
+    cd /opt/MethylDackel/MethylDackel-0.2.1 && \
+    make && \
+    make install prefix=/usr/local/bin && \
+    rm /opt/MethylDackel/MethylDackel.zip
+
+# Install MultiQC
+RUN pip install multiqc

From 29331ea2933a9a418201b5d554373a6461e3d959 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 31 Aug 2017 09:45:14 +0200
Subject: [PATCH 06/11] Refactor all configs. Use singularity for UPPMAX.

---
 Dockerfile               |   3 +
 Dockerfile-bwa           |   6 +-
 conf/aws.config          | 152 ++--------------------------
 conf/base.config         |  92 +++++++++++++++++
 conf/docker.config       |  23 -----
 conf/igenomes.config     | 105 ++++++++++++++++++++
 conf/testing.config      |   3 -
 conf/uppmax-devel.config | 197 +-----------------------------------
 conf/uppmax.config       | 210 +++------------------------------------
 nextflow.config          |  27 ++++-
 10 files changed, 255 insertions(+), 563 deletions(-)
 create mode 100644 conf/base.config
 delete mode 100644 conf/docker.config
 create mode 100644 conf/igenomes.config

diff --git a/Dockerfile b/Dockerfile
index a9d21a5c..69ed3418 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -79,3 +79,6 @@ RUN mkdir /opt/Qualimap && \
 
 # Install MultiQC
 RUN pip install git+https://github.com/ewels/MultiQC.git
+
+# Create UPPMAX directories for Singularity
+RUN mkdir /pica /proj /sw
diff --git a/Dockerfile-bwa b/Dockerfile-bwa
index fa3aac87..431cd9c3 100644
--- a/Dockerfile-bwa
+++ b/Dockerfile-bwa
@@ -1,4 +1,5 @@
-FROM openjdk:8
+# openjdk:8 moved from debian jessie to stretch after u131, which breaks everything (bowtie)
+FROM openjdk:8u121
 
 LABEL authors="phil.ewels@scilifelab.se,denis.moreno@scilifelab.se" \
     description="Docker image containing all requirements for NGI-MethylSeq pipeline"
@@ -89,3 +90,6 @@ RUN mkdir /opt/MethylDackel && \
 
 # Install MultiQC
 RUN pip install multiqc
+
+# Create UPPMAX directories for Singularity
+RUN mkdir /pica /proj /sw
diff --git a/conf/aws.config b/conf/aws.config
index 8795b557..b52c4dec 100644
--- a/conf/aws.config
+++ b/conf/aws.config
@@ -16,153 +16,15 @@ docker {
 process {
   container = 'scilifelab/ngi-methylseq'
   executor = 'ignite'
-  time = { 2.h * task.attempt }
-  errorStrategy = { task.exitStatus == 143 ? 'retry' : 'finish' }
-  maxRetries = 3
-  maxErrors = '-1'
-
-
-  errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'finish' }
-  maxRetries = 3
-  maxErrors = '-1'
-
-  // Process resource requirements
-  $makeBismarkIndex {
-    time = { 36.h * task.attempt }
-  }
-  $fastqc {
-    errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
-  }
-  $trim_galore {
-    time = { 12.h * task.attempt }
-  }
-  $bismark_align {
-    time = { 36.h * task.attempt }
-  }
-  $bismark_deduplicate {
-    time = { 12.h * task.attempt }
-  }
-  $bismark_methXtract {
-    time = { 8.h * task.attempt }
-  }
-  $bismark_report {
-    errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
-  }
-  $bismark_summary {
-    errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
-  }
-  $qualimap {
-    time = { 6.h * task.attempt }
-    errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
-  }
-  $get_software_versions {
-    errorStrategy = 'ignore'
-  }
-  $multiqc {
-    errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
-  }
-
-  $bwamem_align {
-    time = { 24.h * task.attempt }
-  }
-  $samtools_sort {
-    time = { 8.h * task.attempt }
-  }
-
 }
 
 params {
   saveReference = true
-  // illumina iGenomes reference file paths on AWS
-  genomes {
-    'GRCh37' {
-      bismark = 's3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta'
-    }
-    'GRCm38' {
-      bismark = 's3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta'
-    }
-    'TAIR10' {
-      bismark = 's3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta'
-    }
-    'EB2' {
-      bismark = 's3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta'
-    }
-    'UMD3.1' {
-      bismark = 's3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta'
-    }
-    'WBcel235' {
-      bismark = 's3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta'
-    }
-    'CanFam3.1' {
-      bismark = 's3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta'
-    }
-    'GRCz10' {
-      bismark = 's3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta'
-    }
-    'BDGP6' {
-      bismark = 's3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta'
-    }
-    'EquCab2' {
-      bismark = 's3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta'
-    }
-    'EB1' {
-      bismark = 's3://ngi-igenomes/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta'
-    }
-    'Galgal4' {
-      bismark = 's3://ngi-igenomes/igenomes/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta'
-    }
-    'Gm01' {
-      bismark = 's3://ngi-igenomes/igenomes/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta'
-    }
-    'Mmul_1' {
-      bismark = 's3://ngi-igenomes/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta'
-    }
-    'IRGSP-1.0' {
-      bismark = 's3://ngi-igenomes/igenomes/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta'
-    }
-    'CHIMP2.1.4' {
-      bismark = 's3://ngi-igenomes/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta'
-    }
-    'Rnor_6.0' {
-      bismark = 's3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta'
-    }
-    'R64-1-1' {
-      bismark = 's3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta'
-    }
-    'EF2' {
-      bismark = 's3://ngi-igenomes/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta'
-    }
-    'Sbi1' {
-      bismark = 's3://ngi-igenomes/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta'
-    }
-    'Sscrofa10.2' {
-      bismark = 's3://ngi-igenomes/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta'
-    }
-    'AGPv3' {
-      bismark = 's3://ngi-igenomes/igenomes/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex'
-      fasta   = 's3://ngi-igenomes/igenomes/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta'
-    }
-  }
-
+  igenomes_base = 's3://ngi-igenomes/igenomes/'
+  // Max resources based on a typical AWS m4.4xlarge EC2 instance
+  // Customise with --max_memory, --max_cpus and --max_time (or overwrite with another config file)
+  // For example, for m4.2xlarge, use `--max_cpus 8 --max_memory 32`
+  max_memory = 64.GB
+  max_cpus = 16
+  max_time = 240.h
 }
diff --git a/conf/base.config b/conf/base.config
new file mode 100644
index 00000000..254f32e9
--- /dev/null
+++ b/conf/base.config
@@ -0,0 +1,92 @@
+/*
+vim: syntax=groovy
+-*- mode: groovy;-*-
+ * -------------------------------------------------
+ *  Base Nextflow config file
+ * -------------------------------------------------
+ * This file contains basic process requirement setup
+ * It DOES NOT contain any config for cluster, so will run
+ * in default mode by itself. It should be used with
+ * the max_memory, max_cpus and max_time params for
+ * customising hardware limits
+ */
+
+process {
+  cpus = { check_max(1 * task.attempt, 'cpus') }
+  memory = { check_max( 8.GB * task.attempt, 'memory') }
+  time = { check_max(2.h * task.attempt, 'time') }
+
+  errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'finish' }
+  maxRetries = 3
+  maxErrors = '-1'
+
+  // Resource requirements
+  $makeBismarkIndex {
+    cpus = { check_max(8 * task.attempt, 'cpus') }
+    memory = { check_max( 64.GB * task.attempt, 'memory') }
+    time = { check_max(36.h * task.attempt, 'time') }
+  }
+  $fastqc {
+    errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
+  }
+  $trim_galore {
+    cpus = { check_max(2 * task.attempt, 'cpus') }
+    memory = { check_max( 16.GB * task.attempt, 'memory') }
+    time = { check_max(12.h * task.attempt, 'time') }
+  }
+  $bismark_align {
+    cpus = { check_max(8 * task.attempt, 'cpus') }
+    memory = { check_max( 64.GB * task.attempt, 'memory') }
+    time = { check_max(36.h * task.attempt, 'time') }
+  }
+  $bismark_deduplicate {
+    cpus = { check_max(8 * task.attempt, 'cpus') }
+    memory = { check_max( 64.GB * task.attempt, 'memory') }
+    time = { check_max(12.h * task.attempt, 'time') }
+  }
+  $bismark_methXtract {
+    cpus = { check_max(4 * task.attempt, 'cpus') }
+    memory = { check_max( 32.GB * task.attempt, 'memory') }
+    time = { check_max(8.h * task.attempt, 'time') }
+  }
+  $bismark_report {
+    errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
+  }
+  $bismark_summary {
+    errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
+  }
+  $qualimap {
+    cpus = { check_max(4 * task.attempt, 'cpus') }
+    memory = { check_max( 32.GB * task.attempt, 'memory') }
+    time = { check_max(6.h * task.attempt, 'time') }
+    errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
+  }
+  $get_software_versions {
+    executor = 'local'
+    errorStrategy = 'ignore'
+  }
+  $multiqc {
+    executor = 'local'
+    errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
+  }
+
+  $bwamem_align {
+    cpus = { check_max(8 * task.attempt, 'cpus') }
+    memory = { check_max( 64.GB * task.attempt, 'memory') }
+    time = { check_max(24.h * task.attempt, 'time') }
+  }
+  $samtools_sort {
+    cpus = { check_max(4 * task.attempt, 'cpus') }
+    memory = { check_max( 32.GB * task.attempt, 'memory') }
+    time = { check_max(8.h * task.attempt, 'time') }
+  }
+  $markDuplicates {
+    cpus = { check_max(4 * task.attempt, 'cpus') }
+    memory = { check_max( 32.GB * task.attempt, 'memory') }
+  }
+  $methyldackel {
+    cpus = { check_max(6 * task.attempt, 'cpus') }
+    memory = { check_max( 48.GB * task.attempt, 'memory') }
+  }
+
+}
\ No newline at end of file
diff --git a/conf/docker.config b/conf/docker.config
deleted file mode 100644
index a4198b6a..00000000
--- a/conf/docker.config
+++ /dev/null
@@ -1,23 +0,0 @@
-/*
-vim: syntax=groovy
--*- mode: groovy;-*-
- * -------------------------------------------------
- *  Nextflow config file for use with Docker
- * -------------------------------------------------
- * Defines basic usage limits and docker image id.
- * Imported under the default 'docker' Nextflow
- * profile in nextflow.config
- * NOTE: Not suitable for production use, assumes
- * compute limits of only 16GB memory and 1 CPU core.
- */
-
-docker {
-  enabled = true
-}
-
-process {
-  container = 'scilifelab/ngi-methylseq'
-  cpus = 1
-  memory = 16.GB
-  time = 48.h
-}
diff --git a/conf/igenomes.config b/conf/igenomes.config
new file mode 100644
index 00000000..8fb82ad8
--- /dev/null
+++ b/conf/igenomes.config
@@ -0,0 +1,105 @@
+/*
+vim: syntax=groovy
+-*- mode: groovy;-*-
+ * -------------------------------------------------
+ *  Nextflow config file for iGenomes paths
+ * -------------------------------------------------
+ * Defines reference genomes, using iGenome paths
+ * Can be used by any config that customises the base
+ * path using $params.igenomes_base / --igenomes_base
+ */
+
+params {
+  // illumina iGenomes reference file paths on UPPMAX
+  igenomes_base = './iGenomes/'
+  genomes {
+    'GRCh37' {
+      bismark = { "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta" }
+    }
+    'GRCm38' {
+      bismark = { "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta" }
+    }
+    'TAIR10' {
+      bismark = { "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta" }
+    }
+    'EB2' {
+      bismark = { "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta" }
+    }
+    'UMD3.1' {
+      bismark = { "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta" }
+    }
+    'WBcel235' {
+      bismark = { "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta" }
+    }
+    'CanFam3.1' {
+      bismark = { "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta" }
+    }
+    'GRCz10' {
+      bismark = { "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta" }
+    }
+    'BDGP6' {
+      bismark = { "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta" }
+    }
+    'EquCab2' {
+      bismark = { "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta" }
+    }
+    'EB1' {
+      bismark = { "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta" }
+    }
+    'Galgal4' {
+      bismark = { "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta" }
+    }
+    'Gm01' {
+      bismark = { "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta" }
+    }
+    'Mmul_1' {
+      bismark = { "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta" }
+    }
+    'IRGSP-1.0' {
+      bismark = { "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta" }
+    }
+    'CHIMP2.1.4' {
+      bismark = { "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta" }
+    }
+    'Rnor_6.0' {
+      bismark = { "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta" }
+    }
+    'R64-1-1' {
+      bismark = { "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta" }
+    }
+    'EF2' {
+      bismark = { "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta" }
+    }
+    'Sbi1' {
+      bismark = { "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta" }
+    }
+    'Sscrofa10.2' {
+      bismark = { "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta" }
+    }
+    'AGPv3' {
+      bismark = { "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex" }
+      fasta   = { "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta" }
+    }
+  }
+}
diff --git a/conf/testing.config b/conf/testing.config
index e241ce95..f1130102 100644
--- a/conf/testing.config
+++ b/conf/testing.config
@@ -8,9 +8,6 @@ vim: syntax=groovy
 
 docker {
   enabled = true
-  // Fixes Docker mount point error on travis.
-  // Can be removed after Nextflow v0.25.1 is released
-  writableInputMounts = true
 }
 process {
   container = 'scilifelab/ngi-methylseq'
diff --git a/conf/uppmax-devel.config b/conf/uppmax-devel.config
index 3126ef40..3239a0ac 100644
--- a/conf/uppmax-devel.config
+++ b/conf/uppmax-devel.config
@@ -16,202 +16,13 @@ executor {
 }
 
 process {
-  executor = 'slurm'
   queue = 'devcore'
-  cpus = { 1 * task.attempt }
-  memory = { 8.GB * task.attempt }
-  time = 1.h
-  clusterOptions = { "-A $params.project ${params.clusterOptions ?: ''}" }
-
-  errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'finish' }
-  maxRetries = 3
-  maxErrors = '-1'
-
-  // Environment modules and resource requirements
-  $makeBismarkIndex {
-    module = ['bioinfo-tools', 'samtools/1.3', 'bismark']
-    cpus = { 8 * task.attempt }
-    memory = { 64.GB * task.attempt }
-  }
-  $fastqc {
-    module = ['bioinfo-tools', 'FastQC']
-    errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
-  }
-  $trim_galore {
-    module = ['bioinfo-tools', 'TrimGalore']
-    cpus = { 2 * task.attempt }
-    memory = { 16.GB * task.attempt }
-  }
-  $bismark_align {
-    module = ['bioinfo-tools', 'samtools/1.3', 'bismark']
-    cpus = { 8 * task.attempt }
-    memory = { 64.GB * task.attempt }
-  }
-  $bismark_deduplicate {
-    module = ['bioinfo-tools', 'samtools/1.3', 'bismark']
-    cpus = { 8 * task.attempt }
-    memory = { 64.GB * task.attempt }
-  }
-  $bismark_methXtract {
-    module = ['bioinfo-tools', 'samtools/1.3', 'bismark']
-    cpus = { 4 * task.attempt }
-    memory = { 32.GB * task.attempt }
-  }
-  $bismark_report {
-    module = ['bioinfo-tools', 'bismark']
-    errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
-  }
-  $bismark_summary {
-    module = ['bioinfo-tools', 'bismark']
-    errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
-  }
-  $qualimap {
-    module = ['bioinfo-tools', 'samtools/1.3', 'QualiMap']
-    cpus = { 4 * task.attempt }
-    memory = { 32.GB * task.attempt }
-    errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
-  }
-  $get_software_versions {
-    errorStrategy = 'ignore'
-    module = ['bioinfo-tools', 'FastQC', 'TrimGalore', 'samtools/1.3', 'bismark', 'QualiMap', 'MultiQC']
-  }
-  // NB: Overwrite this in a config file in the working directory (nextflow.config) or with -c
-  // if you have your own installation of MultiQC outside of the environment module system.
-  // eg: Add the line: process.$multiqc.module = []
-  $multiqc {
-    module = ['bioinfo-tools', 'MultiQC']
-    executor = 'local'
-    errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
-  }
-
-  $makeBwaMemIndex {
-    module = ['bioinfo-tools', 'bwa', 'bwa-meth', 'samtools/1.3']
-  }
-  $makeFastaIndex {
-    module = ['bioinfo-tools', 'samtools/1.3']
-  }
-  $bwamem_align {
-    module = ['bioinfo-tools', 'bwa', 'bwa-meth', 'samtools/1.3']
-    cpus = { 8 * task.attempt }
-    memory = { 64.GB * task.attempt }
-  }
-  $samtools_flagstat {
-    module = ['bioinfo-tools', 'samtools/1.3']
-  }
-  $samtools_sort {
-    module = ['bioinfo-tools', 'samtools/1.3']
-    cpus = { 4 * task.attempt }
-    memory = { 32.GB * task.attempt }
-  }
-  $samtools_index {
-    module = ['bioinfo-tools', 'samtools/1.3']
-  }
-  $markDuplicates {
-    module = ['bioinfo-tools', 'picard/2.0.1']
-    cpus = { 4 * task.attempt }
-    memory = { 32.GB * task.attempt }
-  }
-  $methyldackel {
-    module = ['bioinfo-tools', 'MethylDackel']
-    cpus = { 6 * task.attempt }
-    memory = { 48.GB * task.attempt }
-  }
-
 }
 
 params {
-  clusterOptions = false
-  params.saveReference = true
-  // illumina iGenomes reference file paths on UPPMAX
-  genomes {
-    'GRCh37' {
-      bismark = '/sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta'
-    }
-    'GRCm38' {
-      bismark = '/sw/data/uppnex/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta'
-    }
-    'TAIR10' {
-      bismark = '/sw/data/uppnex/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta'
-    }
-    'EB2' {
-      bismark = '/sw/data/uppnex/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta'
-    }
-    'UMD3.1' {
-      bismark = '/sw/data/uppnex/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta'
-    }
-    'WBcel235' {
-      bismark = '/sw/data/uppnex/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta'
-    }
-    'CanFam3.1' {
-      bismark = '/sw/data/uppnex/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta'
-    }
-    'GRCz10' {
-      bismark = '/sw/data/uppnex/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta'
-    }
-    'BDGP6' {
-      bismark = '/sw/data/uppnex/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta'
-    }
-    'EquCab2' {
-      bismark = '/sw/data/uppnex/igenomes/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta'
-    }
-    'EB1' {
-      bismark = '/sw/data/uppnex/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta'
-    }
-    'Galgal4' {
-      bismark = '/sw/data/uppnex/igenomes/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta'
-    }
-    'Gm01' {
-      bismark = '/sw/data/uppnex/igenomes/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta'
-    }
-    'Mmul_1' {
-      bismark = '/sw/data/uppnex/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta'
-    }
-    'IRGSP-1.0' {
-      bismark = '/sw/data/uppnex/igenomes/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta'
-    }
-    'CHIMP2.1.4' {
-      bismark = '/sw/data/uppnex/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta'
-    }
-    'Rnor_6.0' {
-      bismark = '/sw/data/uppnex/igenomes/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta'
-    }
-    'R64-1-1' {
-      bismark = '/sw/data/uppnex/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta'
-    }
-    'EF2' {
-      bismark = '/sw/data/uppnex/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta'
-    }
-    'Sbi1' {
-      bismark = '/sw/data/uppnex/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta'
-    }
-    'Sscrofa10.2' {
-      bismark = '/sw/data/uppnex/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta'
-    }
-    'AGPv3' {
-      bismark = '/sw/data/uppnex/igenomes/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta'
-    }
-  }
+  // Max resources to be requested by a devel job
+  max_memory = 120.GB
+  max_cpus = 16
+  max_time = 1.h
 }
 
diff --git a/conf/uppmax.config b/conf/uppmax.config
index be2b3dcc..53b2c9db 100644
--- a/conf/uppmax.config
+++ b/conf/uppmax.config
@@ -4,215 +4,31 @@ vim: syntax=groovy
  * -------------------------------------------------
  *  Nextflow config file for UPPMAX (milou / irma)
  * -------------------------------------------------
- * Defines reference genomes, using iGenome paths
  * Imported under the default 'standard' Nextflow
  * profile in nextflow.config
  */
 
+singularity {
+  autoMounts = true
+  enabled = true
+}
 
 process {
   executor = 'slurm'
-  cpus = { 1 * task.attempt }
-  memory = { 8.GB * task.attempt }
-  time = { 2.h * task.attempt }
   clusterOptions = { "-A $params.project ${params.clusterOptions ?: ''}" }
 
-  errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'finish' }
-  maxRetries = 3
-  maxErrors = '-1'
-
-  // Environment modules and resource requirements
-  $makeBismarkIndex {
-    module = ['bioinfo-tools', 'samtools/1.3', 'bismark']
-    cpus = { 8 * task.attempt }
-    memory = { 64.GB * task.attempt }
-    time = { 36.h * task.attempt }
-  }
-  $fastqc {
-    module = ['bioinfo-tools', 'FastQC']
-    errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
-  }
-  $trim_galore {
-    module = ['bioinfo-tools', 'TrimGalore']
-    cpus = { 2 * task.attempt }
-    memory = { 16.GB * task.attempt }
-    time = { 12.h * task.attempt }
-  }
-  $bismark_align {
-    module = ['bioinfo-tools', 'samtools/1.3', 'bismark']
-    cpus = { 8 * task.attempt }
-    memory = { 64.GB * task.attempt }
-    time = { 36.h * task.attempt }
-  }
-  $bismark_deduplicate {
-    module = ['bioinfo-tools', 'samtools/1.3', 'bismark']
-    cpus = { 8 * task.attempt }
-    memory = { 64.GB * task.attempt }
-    time = { 12.h * task.attempt }
-  }
-  $bismark_methXtract {
-    module = ['bioinfo-tools', 'samtools/1.3', 'bismark']
-    cpus = { 4 * task.attempt }
-    memory = { 32.GB * task.attempt }
-    time = { 8.h * task.attempt }
-  }
-  $bismark_report {
-    module = ['bioinfo-tools', 'bismark']
-    errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
-  }
-  $bismark_summary {
-    module = ['bioinfo-tools', 'bismark']
-    errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
-  }
-  $qualimap {
-    module = ['bioinfo-tools', 'samtools/1.3', 'QualiMap']
-    cpus = { 4 * task.attempt }
-    memory = { 32.GB * task.attempt }
-    time = { 6.h * task.attempt }
-    errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
-  }
-  $get_software_versions {
-    errorStrategy = 'ignore'
-    module = ['bioinfo-tools', 'FastQC', 'TrimGalore', 'samtools/1.3', 'bismark', 'QualiMap', 'MultiQC']
-  }
-  // NB: Overwrite this in a config file in the working directory (nextflow.config) or with -c
-  // if you have your own installation of MultiQC outside of the environment module system.
-  // eg: Add the line: process.$multiqc.module = []
-  $multiqc {
-    module = ['bioinfo-tools', 'MultiQC']
-    executor = 'local'
-    errorStrategy = { ( task.exitStatus == 143 || task.exitStatus == 137 ) ? 'retry' : 'ignore' }
-  }
-
-  $makeBwaMemIndex {
-    module = ['bioinfo-tools', 'bwa', 'bwa-meth', 'samtools/1.3']
-  }
-  $makeFastaIndex {
-    module = ['bioinfo-tools', 'samtools/1.3']
-  }
-  $bwamem_align {
-    module = ['bioinfo-tools', 'bwa', 'bwa-meth', 'samtools/1.3']
-    cpus = { 8 * task.attempt }
-    memory = { 64.GB * task.attempt }
-    time = { 24.h * task.attempt }
-  }
-  $samtools_flagstat {
-    module = ['bioinfo-tools', 'samtools/1.3']
-  }
-  $samtools_sort {
-    module = ['bioinfo-tools', 'samtools/1.3']
-    cpus = { 4 * task.attempt }
-    memory = { 32.GB * task.attempt }
-    time = { 8.h * task.attempt }
-  }
-  $samtools_index {
-    module = ['bioinfo-tools', 'samtools/1.3']
-  }
-  $markDuplicates {
-    module = ['bioinfo-tools', 'picard/2.0.1']
-    cpus = { 4 * task.attempt }
-    memory = { 32.GB * task.attempt }
-  }
-  $methyldackel {
-    module = ['bioinfo-tools', 'MethylDackel']
-    cpus = { 6 * task.attempt }
-    memory = { 48.GB * task.attempt }
-  }
-
+  // Use dockerhub container for singularity
+  container = 'docker://scilifelab/ngi-methylseq'
 }
 
 params {
   clusterOptions = false
-  params.saveReference = true
+  saveReference = true
+  // Max resources requested by a normal node on milou. If you need more memory, run on a fat node using:
+  //   --clusterOptions "-C mem512GB" --max_memory "512GB"
+  max_memory = 128.GB
+  max_cpus = 16
+  max_time = 240.h
   // illumina iGenomes reference file paths on UPPMAX
-  genomes {
-    'GRCh37' {
-      bismark = '/sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta'
-    }
-    'GRCm38' {
-      bismark = '/sw/data/uppnex/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta'
-    }
-    'TAIR10' {
-      bismark = '/sw/data/uppnex/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta'
-    }
-    'EB2' {
-      bismark = '/sw/data/uppnex/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta'
-    }
-    'UMD3.1' {
-      bismark = '/sw/data/uppnex/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta'
-    }
-    'WBcel235' {
-      bismark = '/sw/data/uppnex/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta'
-    }
-    'CanFam3.1' {
-      bismark = '/sw/data/uppnex/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta'
-    }
-    'GRCz10' {
-      bismark = '/sw/data/uppnex/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta'
-    }
-    'BDGP6' {
-      bismark = '/sw/data/uppnex/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta'
-    }
-    'EquCab2' {
-      bismark = '/sw/data/uppnex/igenomes/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta'
-    }
-    'EB1' {
-      bismark = '/sw/data/uppnex/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta'
-    }
-    'Galgal4' {
-      bismark = '/sw/data/uppnex/igenomes/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta'
-    }
-    'Gm01' {
-      bismark = '/sw/data/uppnex/igenomes/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta'
-    }
-    'Mmul_1' {
-      bismark = '/sw/data/uppnex/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta'
-    }
-    'IRGSP-1.0' {
-      bismark = '/sw/data/uppnex/igenomes/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta'
-    }
-    'CHIMP2.1.4' {
-      bismark = '/sw/data/uppnex/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta'
-    }
-    'Rnor_6.0' {
-      bismark = '/sw/data/uppnex/igenomes/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta'
-    }
-    'R64-1-1' {
-      bismark = '/sw/data/uppnex/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta'
-    }
-    'EF2' {
-      bismark = '/sw/data/uppnex/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta'
-    }
-    'Sbi1' {
-      bismark = '/sw/data/uppnex/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta'
-    }
-    'Sscrofa10.2' {
-      bismark = '/sw/data/uppnex/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta'
-    }
-    'AGPv3' {
-      bismark = '/sw/data/uppnex/igenomes/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex'
-      fasta   = '/sw/data/uppnex/igenomes/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta'
-    }
-  }
+  igenomes_base = '/sw/data/uppnex/igenomes/'
 }
diff --git a/nextflow.config b/nextflow.config
index b0b13a76..bb55f56f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -13,15 +13,22 @@ vim: syntax=groovy
 profiles {
 
   standard {
+    includeConfig 'conf/base.config'
+    includeConfig 'conf/igenomes.config'
     includeConfig 'conf/uppmax.config'
   }
   devel {
+    includeConfig 'conf/base.config'
+    includeConfig 'conf/igenomes.config'
+    includeConfig 'conf/uppmax.config'
     includeConfig 'conf/uppmax-devel.config'
   }
   docker {
     includeConfig 'conf/docker.config'
   }
   aws {
+    includeConfig 'conf/base.config'
+    includeConfig 'conf/igenomes.config'
     includeConfig 'conf/aws.config'
   }
   testing {
@@ -47,4 +54,22 @@ manifest {
   homePage = 'https://github.com/SciLifeLab/NGI-MethylSeq'
   description = 'Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.'
   mainScript = 'bismark.nf'
-}
\ No newline at end of file
+}
+
+// Function to ensure that resource requirements don't go beyond
+// a maximum limit
+def check_max(obj, type) {
+  if(type == 'memory'){
+    if(obj.compareTo(params.max_memory))
+      return params.max_memory
+    else
+      return obj
+  } else if(type == 'time'){
+    if(obj.compareTo(params.max_time))
+      return params.max_time
+    else
+      return obj
+  } else if(type == 'cpus'){
+    return Math.min( obj, params.max_cpus )
+  }
+}

From 924482a7b7bae09cb85dfc7b4929813e7d70747c Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 31 Aug 2017 09:52:35 +0200
Subject: [PATCH 07/11] Run travis tests in parallel. Remove docker as
 requirement in test script.

---
 .travis.yml                           | 15 +++++++++------
 tests/{docker_test.sh => run_test.sh} |  1 -
 2 files changed, 9 insertions(+), 7 deletions(-)
 rename tests/{docker_test.sh => run_test.sh} (95%)

diff --git a/.travis.yml b/.travis.yml
index 6e9d9566..8af662f7 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -14,10 +14,13 @@ install:
   - sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
   - cd ${TRAVIS_BUILD_DIR}/tests/
 
+env:
+  - CLFLAGS=""       # Basic run
+  - CLFLAGS="-b"     # Run, build reference genome
+  - CLFLAGS="-r"     # Run, RRBS mode
+  - CLFLAGS="-n"     # Run, no-trimming mode
+  - CLFLAGS="-p"     # BWAmeth use existing ref genome
+  - CLFLAGS="-p -b"  # BWAmeth run, build reference genome
+
 script:
-  - "./docker_test.sh"        # Basic run
-  - "./docker_test.sh -b"     # Run, build reference genome
-  - "./docker_test.sh -r"     # Run, RRBS mode
-  - "./docker_test.sh -n"     # Run, no-trimming mode
-  - "./docker_test.sh -p"     # BWAmeth use existing ref genome
-  - "./docker_test.sh -p -b"  # BWAmeth run, build reference genome
+  - "./run_test.sh $CLFLAGS"
diff --git a/tests/docker_test.sh b/tests/run_test.sh
similarity index 95%
rename from tests/docker_test.sh
rename to tests/run_test.sh
index c7fb8fb0..9092efb8 100755
--- a/tests/docker_test.sh
+++ b/tests/run_test.sh
@@ -16,7 +16,6 @@ function print_usage {
 # Check that we have required commands
 curl --version >/dev/null 2>&1 || { echo >&2 "I require curl, but it's not installed. Aborting."; exit 1; }
 tar --version >/dev/null 2>&1 || { echo >&2 "I require tar, but it's not installed. Aborting."; exit 1; }
-docker -v >/dev/null 2>&1 || { echo >&2 "I require docker, but it's not installed. Visit https://www.docker.com/products/overview#/install_the_platform  ."; exit 1; }
 nextflow -v >/dev/null 2>&1 || { echo >&2 "I require nextflow, but it's not installed. If you hava Java, run 'curl -fsSL get.nextflow.io | bash'. If not, install Java."; exit 1; }
 
 # Detect Travis fork for dockerhub image if we can

From f6e4be9668dabb560cb852868a3c7265f70ccf94 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 31 Aug 2017 09:59:32 +0200
Subject: [PATCH 08/11] Added option to specify singularity image in test
 script.

---
 tests/run_test.sh | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/tests/run_test.sh b/tests/run_test.sh
index 9092efb8..fc909d26 100755
--- a/tests/run_test.sh
+++ b/tests/run_test.sh
@@ -10,6 +10,7 @@ function print_usage {
     "\t\t[-u (run UPPMAX test)\n" \
     "\t\t[-t <test data directory>]\n" \
     "\t\t[-d <docker image>]\n" \
+    "\t\t[-s <singularity image>]\n" \
     "\t\t[-h (show this help message)]" >&2 ;
 }
 
@@ -41,8 +42,9 @@ profile="-profile testing"
 refs="--bismark_index ${data_dir}/references/BismarkIndex/"
 rrbs=""
 notrim=""
+singularityfl=""
 
-while getopts ":brnpuht:d:" opt; do
+while getopts ":brnpuht:d:s:" opt; do
   case $opt in
     b)
       echo "Building genome references" >&2
@@ -77,6 +79,10 @@ while getopts ":brnpuht:d:" opt; do
       echo "Using docker image $OPTARG" >&2
       dockerfl="-with-docker $OPTARG"
       ;;
+    s)
+      echo "Using singularity image $OPTARG" >&2
+      singularityfl="-with-singularity $OPTARG"
+      ;;
     h)
       print_usage
       exit
@@ -113,7 +119,7 @@ fi
 # Run name
 run_name="Test MethylSeq Run: "$(date +%s)
 
-cmd="nextflow run $pipelinescript -resume -name \"$run_name\" $profile $notrim $rrbs $dockerfl $refs --singleEnd --reads \"${data_dir}/*.fastq.gz\""
+cmd="nextflow run $pipelinescript -resume -name \"$run_name\" $profile $notrim $rrbs $dockerfl $singularityfl $refs --singleEnd --reads \"${data_dir}/*.fastq.gz\""
 echo "Starting nextflow... Command:"
 echo $cmd
 echo "-------------------------------------------------------"

From 3b0ae668acf578e2475fd21d408c3f9c54093c2f Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Thu, 31 Aug 2017 10:26:28 +0200
Subject: [PATCH 09/11] Add in default params to base config.

---
 conf/base.config | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/conf/base.config b/conf/base.config
index 254f32e9..c9596269 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -88,5 +88,11 @@ process {
     cpus = { check_max(6 * task.attempt, 'cpus') }
     memory = { check_max( 48.GB * task.attempt, 'memory') }
   }
+}
 
-}
\ No newline at end of file
+params {
+  // Defaults only, expecting to be overwritten
+  max_memory = 128.GB
+  max_cpus = 16
+  max_time = 240.h
+}

From 44c30e35f5690124d7b681d60f81f710c36bfc08 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 1 Sep 2017 12:02:22 +0200
Subject: [PATCH 10/11] Removed autoMounts from singularity support.

---
 conf/uppmax.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/conf/uppmax.config b/conf/uppmax.config
index 53b2c9db..3268dd4d 100644
--- a/conf/uppmax.config
+++ b/conf/uppmax.config
@@ -9,7 +9,6 @@ vim: syntax=groovy
  */
 
 singularity {
-  autoMounts = true
   enabled = true
 }
 

From ae3e5e7004a1729a4688eebc3cd0736615de7047 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Fri, 1 Sep 2017 12:23:06 +0200
Subject: [PATCH 11/11] Comment out BWA-meth tests until I figure out how to
 handle docker images properly.

---
 .travis.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 8af662f7..d45c6220 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -19,8 +19,9 @@ env:
   - CLFLAGS="-b"     # Run, build reference genome
   - CLFLAGS="-r"     # Run, RRBS mode
   - CLFLAGS="-n"     # Run, no-trimming mode
-  - CLFLAGS="-p"     # BWAmeth use existing ref genome
-  - CLFLAGS="-p -b"  # BWAmeth run, build reference genome
+  # Commented out until I figure out how to handle multiple docker images nicely
+  # - CLFLAGS="-p"     # BWAmeth use existing ref genome
+  # - CLFLAGS="-p -b"  # BWAmeth run, build reference genome
 
 script:
   - "./run_test.sh $CLFLAGS"